Class project for adam2392 and ttomita
https://github.com/Upward-Spiral-Science/data/tree/master/syn-diversity
##Contact Handle: adam2392
Email:ali39@jhu.edu
We are working on synapse diversity within the brain with image data gathered from array tomography.
##ToC
####Assignment 1
./Draft/summary.md
Significance and Feasability analysis of my proposed project topic
####Assignment 2
./draft/questions.md
Asking the 6 types of scientific questions about my project topic
####Assignment 3
./code/descriptive_and_exploratory_answers.ipynb
./Code/Exploratory_analysis_tyler.ipynb
Begin answering my descriptive and exploratory questions. Once I've answered them I will go back and revise the questions I asked - discuss those I couldn't fully answer, ask follow up questions that would be informative, etc.
Updated the questions based on our initial analysis - After Midterm presentation
###Assignment 4
./code/inferential_simulation.ipynb
**./Code/inference_tyler.ipynb*
Formally asked inferential question about my data, and answered it on simulated data from the null model, alternate model, and real data
###Assignment 5
./code/classification_simulation.ipynb
Formally asked classification question about my data, and answered it on simulated data from the alternate model, and real data
###Assignment 6
./code/test_assumptions.ipynb
./Code/assumption_checking_tyler.ipynb
In the previous two assignments, we made assumptions about our data. Now, we will check them and see whether or not they are true, and if not, update our understanding or assumptions about our data to those which are more right.
###Assignment 7
./draft/summary_presentation.pdf
Presentation about findings and methods used throughout the project.
###Assignment 8
./docs/progress_report.md
Report stating all analysis completed to date, as well as logical next steps.
###Assignment 9
[./code/extended_exploratory.ipynb](./Code/newexploring/exploratory analysis.ipynb)
./Code/exploratory_analysis2_tyler.ipynb
10 more questions and plots about my data. Shows a suite of BIC plots for transformed data and filtered data by synap values at 25, 50 and 75%. Did separately for f0, f1, f2, and f3 instead of all together.
###Assignment 10
[./code/multiple_distributions.ipynb](./Code/newexploring/clustering analysis.ipynb)
Testing the clustering with a k of 4, 5, 6 on f0